|
| Status |
Public on Feb 08, 2024 |
| Title |
WT 0.39 U MNase Replicate-1 |
| Sample type |
SRA |
| |
|
| Source name |
yeast
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype: Wildtype
treatment: MNase 0.39 U
|
| Treatment protocol |
After spheroplast and nuclei isolation chromatin was digested with increasing concentrations of MNase (0.39, 1.56, 6.25, 25 and 100 U )
|
| Growth protocol |
Both wildtype and triple deletion strains were grown at 30◦C in YPD media upto OD-2 and crosslinked with 1% formaldehyde.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted by using phenol: chloroform
Size selection was done to exclude fragments of larger size and then the library was prepared as per protocol described in Bowman et al., BMC Genomics (2013)
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
A1
WT- Replicate 1
|
| Data processing |
Using Bowtie aligner2 the sequenced paired-end reads were mapped to the Saccharomyces cerevisiae reference genome((as described in earlier Mieczkowski et al., 2016)
Read frequencies were calculated in non-overlapping bins of 200 bp size for each titration point individually.
Linear regression was fitted on the normalized frequencies in bins and the obtained regression coefficients were used as MACC scores.
Supplementary files format and content: biwig, wig
Supplementary files format and content: bedgraph
|
| |
|
| Submission date |
Dec 13, 2022 |
| Last update date |
Feb 08, 2024 |
| Contact name |
Ajaz ul Hamid Wani |
| E-mail(s) |
ahwani@kashmiruniversity.ac.in
|
| Phone |
9797918365
|
| Organization name |
University of Kashmir
|
| Department |
Biotechnology
|
| Lab |
Genome Organization
|
| Street address |
Hazratbal
|
| City |
Srinagar |
| State/province |
Jammu and Kashmir |
| ZIP/Postal code |
190006 |
| Country |
India |
| |
|
| Platform ID |
GPL17342 |
| Series (1) |
| GSE220880 |
MNase titration-Seq of Saccharomyces cerevisiae. |
|
| Relations |
| BioSample |
SAMN32204533 |
| SRA |
SRX18677200 |
